Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
Entering edit mode
Shane • 0
Last seen 8 weeks ago

Hi all,

I'm currently trying to annotate some methylation data generated with Illumina Infinium HumanMethylation450K. My probs file comes in a .bed format, which I'm using as my values. When running my code,

mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "")
myfilter <- c("chromosome_name", "start", "end")
bed # The file with the probes: chrom_name    start_pos    end_pos
values <- list(bed)

annotated <- getBM(attributes = c("ensembl_gene_id", "ensembl_transcript_id", "strand", "description", "chromosome_name", "start_position",
                          "end_position", "transcript_length", "external_gene_name", "percentage_gene_gc_content",
                          "gene_biotype", "version", "transcript_version"),
                           values = c(values[[1]][1], values[[1]][2], values[[1]][3]), #values[[1]][1]: chrom_name; values[[1]][2]: start_pos; values[[1]][3]: end_pos
                           mart = mart, filters = myfilter)

I'm getting the following Error:

Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery,  : 
  The query to the BioMart webservice returned an invalid result.
The number of columns in the result table does not equal the number of attributes in the query.
Please report this on the support site at

Changing the mirror results in a data frame with an empty output with 0 rows and 13 variables (variables = attributes).

Can anyone help me solving or explain me these problems?

> sessionInfo("biomaRt")
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

attached base packages:

other attached packages:
[1] biomaRt_2.50.0
process annotationTools AnnotationFilter Annotation biomaRt • 81 views

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